{
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  "Package": "MBECS",
  "Title": "Evaluation and correction of batch effects in microbiome\ndata-sets",
  "Version": "1.17.0",
  "Authors@R": "person(given = \"Michael\",\nfamily = \"Olbrich\",\nrole = c(\"aut\", \"cre\"),\nemail = \"M.Olbrich@protonmail.com\",\ncomment = c(ORCID = \"0000-0003-2789-3382\"))",
  "Description": "The Microbiome Batch Effect Correction Suite (MBECS)\nprovides a set of functions to evaluate and mitigate unwated\nnoise due to processing in batches. To that end it incorporates\na host of batch correcting algorithms (BECA) from various\npackages. In addition it offers a correction and reporting\npipeline that provides a preliminary look at the\ncharacteristics of a data-set before and after correcting for\nbatch effects.",
  "biocViews": "BatchEffect, Microbiome, ReportWriting, Visualization,\nNormalization, QualityControl",
  "URL": "https://github.com/rmolbrich/MBECS",
  "BugReports": "https://github.com/rmolbrich/MBECS/issues/new",
  "License": "Artistic-2.0",
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  "Collate": "'MBECS-package.R' 'data.R' 'mbecs_classes.R'\n'mbecs_analyses.R' 'mbecs_corrections.R' 'mbecs_helper.R'\n'mbecs_plots.R' 'mbecs_reports.R'",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:57:55 UTC",
  "RemoteUrl": "https://github.com/bioc/MBECS",
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  "Packaged": {
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    "User": "root"
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  "Author": "Michael Olbrich [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-2789-3382>)",
  "Maintainer": "Michael Olbrich <M.Olbrich@protonmail.com>",
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  "_created": "2026-05-25T06:37:33.000Z",
  "_published": "2026-05-25T06:44:54.208Z",
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    "MbecData",
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    "mbecGetPhyloseq",
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    "mbecHeatPlot",
    "mbecHelpFactor",
    "mbecLM",
    "mbecMixedVariance",
    "mbecModelVariance",
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    "mbecMosaicPlot",
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    "mbecPCAPlot",
    "mbecProcessInput",
    "mbecPVCAStatsPlot",
    "mbecRDAStatsPlot",
    "mbecReportPost",
    "mbecReportPrelim",
    "mbecRLE",
    "mbecRLEPlot",
    "mbecRunCorrections",
    "mbecSCOEFStatsPlot",
    "mbecSetData",
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    "mbecTransform",
    "mbecValidateModel",
    "mbecVarianceStats",
    "mbecVarianceStatsPlot",
    "percentileNorm",
    "poscore"
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      "title": "Mock-up microbiome abundance table and meta-data.",
      "object": "dummy.list",
      "file": "dummy.list.rda",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "dummy.mbec",
      "title": "Mock-up microbiome abundance table and meta-data.",
      "object": "dummy.mbec",
      "file": "dummy.mbec.rda",
      "class": [
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      ],
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      "table": false,
      "tojson": false
    },
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      "name": "dummy.ps",
      "title": "Mock-up microbiome abundance table and meta-data.",
      "object": "dummy.ps",
      "file": "dummy.ps.rda",
      "class": [
        "phyloseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "dot-mbecGetData",
      "title": "Mbec-Data Getter",
      "topics": [
        ".mbecGetData"
      ]
    },
    {
      "page": "dot-mbecGetPhyloseq",
      "title": "Return Phyloseq after correction",
      "topics": [
        ".mbecGetPhyloseq"
      ]
    },
    {
      "page": "dot-mbecSetData",
      "title": "Mbec-Data Setter",
      "topics": [
        ".mbecSetData"
      ]
    },
    {
      "page": "colinScore",
      "title": "Variable Correlation Linear (Mixed) Models",
      "topics": [
        "colinScore"
      ]
    },
    {
      "page": "dummy.list",
      "title": "Mock-up microbiome abundance table and meta-data.",
      "topics": [
        "dummy.list"
      ]
    },
    {
      "page": "dummy.mbec",
      "title": "Mock-up microbiome abundance table and meta-data.",
      "topics": [
        "dummy.mbec"
      ]
    },
    {
      "page": "dummy.ps",
      "title": "Mock-up microbiome abundance table and meta-data.",
      "topics": [
        "dummy.ps"
      ]
    },
    {
      "page": "externalPLSDA",
      "title": "Partial Least Squares Discriminant Analysis Computation",
      "topics": [
        "externalPLSDA"
      ]
    },
    {
      "page": "mbecBat",
      "title": "Combat Batch Effects (ComBat)",
      "topics": [
        "mbecBat"
      ]
    },
    {
      "page": "mbecBMC",
      "title": "Batch Mean Centering (BMC)",
      "topics": [
        "mbecBMC"
      ]
    },
    {
      "page": "mbecBox",
      "title": "Feature Differential Abundance Box-Plot",
      "topics": [
        "mbecBox"
      ]
    },
    {
      "page": "mbecBoxPlot",
      "title": "Variability boxes plotting function",
      "topics": [
        "mbecBoxPlot"
      ]
    },
    {
      "page": "mbecCLR",
      "title": "Centered Log-Ratio Transformation",
      "topics": [
        "mbecCLR"
      ]
    },
    {
      "page": "mbecCorrection",
      "title": "Batch Effect Correction Wrapper",
      "topics": [
        "mbecCorrection"
      ]
    },
    {
      "page": "MbecData",
      "title": "Define MbecData-class",
      "topics": [
        "MbecData"
      ]
    },
    {
      "page": "mbecDeflate",
      "title": "Calculate matrix residuals",
      "topics": [
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      ]
    },
    {
      "page": "mbecDummy",
      "title": "Creates a dummy data-set with abundance matrix and meta-data.",
      "topics": [
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      ]
    },
    {
      "page": "mbecExplainedVariance",
      "title": "Calculate explained variance using CCA",
      "topics": [
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      ]
    },
    {
      "page": "mbecGetData",
      "title": "Mbec-Data Getter",
      "topics": [
        "mbecGetData"
      ]
    },
    {
      "page": "mbecGetData-MbecData-method",
      "title": "Mbec-Data Getter",
      "topics": [
        "mbecGetData,MbecData-method"
      ]
    },
    {
      "page": "mbecGetPhyloseq",
      "title": "Return Phyloseq after correction",
      "topics": [
        "mbecGetPhyloseq"
      ]
    },
    {
      "page": "mbecGetPhyloseq-MbecData-method",
      "title": "Return Phyloseq after correction",
      "topics": [
        "mbecGetPhyloseq,MbecData-method"
      ]
    },
    {
      "page": "mbecHeat",
      "title": "Feature Differential Abundance Heatmap",
      "topics": [
        "mbecHeat"
      ]
    },
    {
      "page": "mbecHeatPlot",
      "title": "Heatmap plotting function",
      "topics": [
        "mbecHeatPlot"
      ]
    },
    {
      "page": "mbecHelpFactor",
      "title": "Check If Covariates Are Factors",
      "topics": [
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      ]
    },
    {
      "page": "mbecLM",
      "title": "Linear (Mixed) Model Feature to Batch Fit",
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    },
    {
      "page": "mbecMixedVariance",
      "title": "Mixed Model Variance-Component Extraction",
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      ]
    },
    {
      "page": "mbecModelVariance",
      "title": "Estimate Explained Variance",
      "topics": [
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      ]
    },
    {
      "page": "mbecModelVarianceLM",
      "title": "Estimate Explained Variance with Linear Models",
      "topics": [
        "mbecModelVarianceLM"
      ]
    },
    {
      "page": "mbecModelVarianceLMM",
      "title": "Estimate Explained Variance with Linear Mixed Models",
      "topics": [
        "mbecModelVarianceLMM"
      ]
    },
    {
      "page": "mbecModelVariancePVCA",
      "title": "Estimate Explained Variance with Principal Variance Component Analysis",
      "topics": [
        "mbecModelVariancePVCA"
      ]
    },
    {
      "page": "mbecModelVarianceRDA",
      "title": "Estimate Explained Variance with Redundancy Analysis",
      "topics": [
        "mbecModelVarianceRDA"
      ]
    },
    {
      "page": "mbecModelVarianceSCOEF",
      "title": "Estimate Explained Variance with Silhouette Coefficient",
      "topics": [
        "mbecModelVarianceSCOEF"
      ]
    },
    {
      "page": "mbecMosaic",
      "title": "Mosaic Sample Group Allocation",
      "topics": [
        "mbecMosaic"
      ]
    },
    {
      "page": "mbecMosaicPlot",
      "title": "Mosaic plotting function",
      "topics": [
        "mbecMosaicPlot"
      ]
    },
    {
      "page": "mbecPCA",
      "title": "Principal Component Analysis Plot",
      "topics": [
        "mbecPCA"
      ]
    },
    {
      "page": "mbecPCA-MbecData-method",
      "title": "Principal Component Analysis Plot for MbecData",
      "topics": [
        "mbecPCA,MbecData-method"
      ]
    },
    {
      "page": "mbecPCAPlot",
      "title": "PCA plotting function",
      "topics": [
        "mbecPCAPlot"
      ]
    },
    {
      "page": "mbecPLSDA",
      "title": "Partial Least Squares Discriminant Analysis",
      "topics": [
        "mbecPLSDA"
      ]
    },
    {
      "page": "mbecPN",
      "title": "Percentile Normalization (PN)",
      "topics": [
        "mbecPN"
      ]
    },
    {
      "page": "mbecProcessInput",
      "title": "Mbec-Data Constructor Wrapper",
      "topics": [
        "mbecProcessInput"
      ]
    },
    {
      "page": "mbecProcessInput-list-method",
      "title": "Mbec-Data Constructor Wrapper",
      "topics": [
        "mbecProcessInput,list-method"
      ]
    },
    {
      "page": "mbecProcessInput-MbecData-method",
      "title": "Mbec-Data Constructor Wrapper",
      "topics": [
        "mbecProcessInput,MbecData-method"
      ]
    },
    {
      "page": "mbecProcessInput-phyloseq-method",
      "title": "Mbec-Data Constructor Wrapper",
      "topics": [
        "mbecProcessInput,phyloseq-method"
      ]
    },
    {
      "page": "mbecPVCAStatsPlot",
      "title": "Plot Proportion of Variance for PVCA",
      "topics": [
        "mbecPVCAStatsPlot"
      ]
    },
    {
      "page": "mbecRBE",
      "title": "Remove Batch Effects (RBE)",
      "topics": [
        "mbecRBE"
      ]
    },
    {
      "page": "mbecRDAStatsPlot",
      "title": "Plot Proportion of Variance for pRDA",
      "topics": [
        "mbecRDAStatsPlot"
      ]
    },
    {
      "page": "mbecReportPost",
      "title": "Constructs a comparative report of batch corrected data.",
      "topics": [
        "mbecReportPost"
      ]
    },
    {
      "page": "mbecReportPrelim",
      "title": "Constructs an initial report of a single data-set.",
      "topics": [
        "mbecReportPrelim"
      ]
    },
    {
      "page": "mbecRLE",
      "title": "Relative Log Expression Plot",
      "topics": [
        "mbecRLE"
      ]
    },
    {
      "page": "mbecRLEPlot",
      "title": "RLE plotting function",
      "topics": [
        "mbecRLEPlot"
      ]
    },
    {
      "page": "mbecRunCorrections",
      "title": "Run Correction Pipeline",
      "topics": [
        "mbecRunCorrections"
      ]
    },
    {
      "page": "mbecRUV2",
      "title": "Remove unwanted Variation 2 (RUV-2)",
      "topics": [
        "mbecRUV2"
      ]
    },
    {
      "page": "mbecRUV3",
      "title": "Remove Unwanted Variation 3 (RUV-3)",
      "topics": [
        "mbecRUV3"
      ]
    },
    {
      "page": "mbecRUV4",
      "title": "Remove Unwanted Variation 4 (RUV-4)",
      "topics": [
        "mbecRUV4"
      ]
    },
    {
      "page": "MBECS",
      "title": "MBECS: Evaluation and correction of batch effects in microbiome data-sets.",
      "topics": [
        "MBECS"
      ]
    },
    {
      "page": "mbecSCOEFStatsPlot",
      "title": "Plot Silhouette Coefficient",
      "topics": [
        "mbecSCOEFStatsPlot"
      ]
    },
    {
      "page": "mbecSetData",
      "title": "Mbec-Data Setter",
      "topics": [
        "mbecSetData"
      ]
    },
    {
      "page": "mbecSetData-MbecData-method",
      "title": "Mbec-Data Setter",
      "topics": [
        "mbecSetData,MbecData-method"
      ]
    },
    {
      "page": "mbecSVA",
      "title": "Surrogate variable Analysis (SVA)",
      "topics": [
        "mbecSVA"
      ]
    },
    {
      "page": "mbecSVD",
      "title": "Singular Value Decomposition (SVD)",
      "topics": [
        "mbecSVD"
      ]
    },
    {
      "page": "mbecTestModel",
      "title": "Check If Model Is Estimable",
      "topics": [
        "mbecTestModel"
      ]
    },
    {
      "page": "mbecTransform",
      "title": "Normalizing Transformations",
      "topics": [
        "mbecTransform"
      ]
    },
    {
      "page": "mbecUpperCase",
      "title": "Capitalize Word Beginning",
      "topics": [
        "mbecUpperCase"
      ]
    },
    {
      "page": "mbecValidateModel",
      "title": "Validate Linear (Mixed) Models",
      "topics": [
        "mbecValidateModel"
      ]
    },
    {
      "page": "mbecVarianceStats",
      "title": "Wrapper for Model Variable Variance Extraction",
      "topics": [
        "mbecVarianceStats"
      ]
    },
    {
      "page": "mbecVarianceStatsLM",
      "title": "Model Variable Variance Extraction from LM",
      "topics": [
        "mbecVarianceStatsLM"
      ]
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      "headings": [
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        "Dependencies",
        "Installation",
        "Workflow",
        "Start from abundance table",
        "Start from phyloseq object",
        "Apply transformations",
        "Preliminary report",
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